KEGG   PATHWAY: pprl03018
Entry
pprl03018                   Pathway                                
Name
RNA degradation - Poeciliopsis prolifica (blackstripe livebearer)
Description
The correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay exist and both pathways are initiated by poly(A) shortening of the mRNA. In the 5' to 3' pathway, this is followed by decapping which then permits the 5' to 3' exonucleolytic degradation of transcripts. In the 3' to 5' pathway, the exosome, a large multisubunit complex, plays a key role. The exosome exists in archaeal cells, too. In bacteria, endoribonuclease E, a key enzyme involved in RNA decay and processing, organizes a protein complex called degradosome. RNase E or R interacts with the phosphate-dependent exoribonuclease polynucleotide phosphorylase, DEAD-box helicases, and additional factors in the RNA-degrading complex.
Class
Genetic Information Processing; Folding, sorting and degradation
Pathway map
pprl03018  RNA degradation
pprl03018

Other DBs
GO: 0006401
Organism
Poeciliopsis prolifica (blackstripe livebearer) [GN:pprl]
Gene
129352860  lsm8; LSM8 homolog, U6 small nuclear RNA associated [KO:K12627]
129352874  [KO:K12605]
129353106  [KO:K00850] [EC:2.7.1.11]
129353657  xrn2; LOW QUALITY PROTEIN: 5'-3' exoribonuclease 2 [KO:K12619] [EC:3.1.13.-]
129353751  cnot10; CCR4-NOT transcription complex subunit 10 isoform X1 [KO:K12607]
129353857  hspa9; stress-70 protein, mitochondrial [KO:K04043]
129354035  eno1b; enolase 1b, (alpha) [KO:K01689] [EC:4.2.1.11]
129354172  exosc7; exosome complex component RRP42 [KO:K12589]
129354182  skic2; helicase SKI2W [KO:K12599] [EC:3.6.4.13]
129354344  [KO:K03681]
129354628  [KO:K12622]
129355541  [KO:K18681] [EC:3.1.13.-]
129355582  [KO:K12617]
129355960  [KO:K12606]
129357666  pfkmb; phosphofructokinase, muscle b [KO:K00850] [EC:2.7.1.11]
129358733  edc4; enhancer of mRNA-decapping protein 4 isoform X1 [KO:K12616]
129358987  ddx6; probable ATP-dependent RNA helicase ddx6 [KO:K12614] [EC:3.6.4.13]
129359224  exosc5; exosome complex component RRP46 [KO:K12590]
129359551  cnot2; CCR4-NOT transcription complex subunit 2 [KO:K12605]
129359862  dis3; exosome complex exonuclease RRP44 [KO:K12585] [EC:3.1.13.-]
129359898  c1d; nuclear nucleic acid-binding protein C1D [KO:K12592]
129360177  [KO:K00962] [EC:2.7.7.8]
129360295  [KO:K03681]
129360391  cnot4a; CCR4-NOT transcription complex subunit 4 [KO:K10643] [EC:2.3.2.27]
129361233  pfkla; ATP-dependent 6-phosphofructokinase, liver type [KO:K00850] [EC:2.7.1.11]
129361436  edc3; enhancer of mRNA-decapping protein 3 [KO:K12615]
129361654  exosc4; exosome complex component RRP41 [KO:K11600]
129362058  xrn1; 5'-3' exoribonuclease 1 [KO:K12618] [EC:3.1.13.-]
129362187  mphosph6; M-phase phosphoprotein 6 [KO:K12593]
129362428  zcchc7; zinc finger CCHC domain-containing protein 7 isoform X1 [KO:K12597]
129362508  cnot6a; CCR4-NOT transcription complex subunit 6a [KO:K12603] [EC:3.1.13.4]
129362827  dcps; m7GpppX diphosphatase [KO:K12584] [EC:3.6.1.59]
129362972  cnot7; CCR4-NOT transcription complex subunit 7 [KO:K12581]
129363249  tob1a; protein Tob1a [KO:K14443]
129363829  [KO:K14443]
129364419  tent4b; terminal nucleotidyltransferase 4B [KO:K03514] [EC:2.7.7.19]
129364668  pfkpa; ATP-dependent 6-phosphofructokinase, platelet type isoform X1 [KO:K00850] [EC:2.7.1.11]
129364784  pan3; PAN2-PAN3 deadenylation complex subunit PAN3 [KO:K12572]
129365223  pabpc4; polyadenylate-binding protein 4 [KO:K13126]
129366056  cnot6l; CCR4-NOT transcription complex subunit 6-like [KO:K12603] [EC:3.1.13.4]
129366397  skic8; SKI8 subunit of superkiller complex protein [KO:K12602]
129366415  exosc2; exosome complex component RRP4 [KO:K03679]
129366895  exosc1; exosome complex component CSL4 isoform X1 [KO:K07573]
129367094  exosc9; exosome complex component RRP45 isoform X1 [KO:K03678]
129367394  [KO:K14443]
129367463  exosc6; exosome complex component MTR3 [KO:K12587]
129367616  [KO:K13126]
129367642  [KO:K03514] [EC:2.7.7.19]
129368800  btg3; protein BTG3 [KO:K14443]
129370013  dhx36; ATP-dependent DNA/RNA helicase DHX36 [KO:K14442] [EC:3.6.4.13]
129370332  [KO:K13126]
129370395  pan2; PAN2-PAN3 deadenylation complex catalytic subunit PAN2 isoform X1 [KO:K12571] [EC:3.1.13.4]
129370613  cnot8; CCR4-NOT transcription complex subunit 8 [KO:K12581]
129370645  btg4; protein BTG4 isoform X1 [KO:K14443]
129371089  smx5; smx5 [KO:K12621]
129371092  cnot3a; CCR4-NOT transcription complex subunit 3a [KO:K12580]
129371752  zgc:103759; U8 snoRNA-decapping enzyme [KO:K16855] [EC:3.6.1.62 3.6.1.64]
129371913  skic3; tetratricopeptide repeat protein 37 isoform X1 [KO:K12600]
129372395  pfkma; phosphofructokinase, muscle a [KO:K00850] [EC:2.7.1.11]
129372450  eno1a; enolase 1a, (alpha) isoform X1 [KO:K01689] [EC:4.2.1.11]
129372537  exosc10; exosome component 10 [KO:K12591] [EC:3.1.13.-]
129372578  dcp1a; mRNA-decapping enzyme 1A [KO:K12610] [EC:3.-.-.-]
129372684  cnot1; CCR4-NOT transcription complex subunit 1 isoform X1 [KO:K12604]
129372794  [KO:K12622]
129373012  lsm1; U6 snRNA-associated Sm-like protein LSm1 [KO:K12620]
129373443  exosc8; exosome complex component RRP43 [KO:K12586]
129374228  mtrex; exosome RNA helicase MTR4 [KO:K12598] [EC:3.6.4.13]
129374516  [KO:K12606]
129374644  lsm7; U6 snRNA-associated Sm-like protein LSm7 [KO:K12626]
129375013  [KO:K13126]
129375574  btg1; protein BTG1 [KO:K14443]
129375630  dcp1b; mRNA-decapping enzyme 1B [KO:K12611] [EC:3.-.-.-]
129375787  [KO:K12614] [EC:3.6.4.13]
129375802  [KO:K01689] [EC:4.2.1.11]
129375941  cnot3b; CCR4-NOT transcription complex subunit 3b [KO:K12580]
129376278  tent4a; LOW QUALITY PROTEIN: terminal nucleotidyltransferase 4A [KO:K03514] [EC:2.7.7.19]
129376677  [KO:K01689] [EC:4.2.1.11]
129376893  parn; poly(A)-specific ribonuclease PARN isoform X1 [KO:K01148] [EC:3.1.13.4]
129377195  lsm4; LOW QUALITY PROTEIN: U6 snRNA-associated Sm-like protein LSm4 [KO:K12623]
129377535  tob1b; protein Tob1b [KO:K14443]
129378979  lsm5; U6 snRNA-associated Sm-like protein LSm5 [KO:K12624]
129379208  hspd1; 60 kDa heat shock protein, mitochondrial [KO:K04077] [EC:5.6.1.7]
129379794  dcp2; m7GpppN-mRNA hydrolase [KO:K12613] [EC:3.6.1.62]
Reference
  Authors
Houseley J, Tollervey D
  Title
The many pathways of RNA degradation.
  Journal
Cell 136:763-76 (2009)
DOI:10.1016/j.cell.2009.01.019
Reference
  Authors
Buttner K, Wenig K, Hopfner KP
  Title
The exosome: a macromolecular cage for controlled RNA degradation.
  Journal
Mol Microbiol 61:1372-9 (2006)
DOI:10.1111/j.1365-2958.2006.05331.x
Reference
  Authors
Schilders G, van Dijk E, Raijmakers R, Pruijn GJ
  Title
Cell and molecular biology of the exosome: how to make or break an RNA.
  Journal
Int Rev Cytol 251:159-208 (2006)
DOI:10.1016/S0074-7696(06)51005-8
Reference
  Authors
Hartung S, Hopfner KP
  Title
The exosome, plugged.
  Journal
EMBO Rep 8:456-7 (2007)
DOI:10.1038/sj.embor.7400961
Reference
  Authors
Carpousis AJ
  Title
The RNA degradosome of Escherichia coli: an mRNA-degrading machine assembled on RNase E.
  Journal
Annu Rev Microbiol 61:71-87 (2007)
DOI:10.1146/annurev.micro.61.080706.093440
Reference
  Authors
Marcaida MJ, DePristo MA, Chandran V, Carpousis AJ, Luisi BF
  Title
The RNA degradosome: life in the fast lane of adaptive molecular evolution.
  Journal
Trends Biochem Sci 31:359-65 (2006)
DOI:10.1016/j.tibs.2006.05.005
Reference
  Authors
Condon C
  Title
Maturation and degradation of RNA in bacteria.
  Journal
Curr Opin Microbiol 10:271-8 (2007)
DOI:10.1016/j.mib.2007.05.008
Related
pathway
pprl03015  mRNA surveillance pathway
KO pathway
ko03018   

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